Freesurfer July 2007

freesurfer@nmr.mgh.harvard.edu

61 participants
99 discussions

Combining annots?
by Morgan Hough 24 Jul '07

24 Jul '07

I have a question about using labels from different annots. The Desikan annot has a large region labeled unknown including medial wall and lateral insula and operculum. The Destrieux annot has a separate medial wall label. Is there an easy way to use the Destrieux annot label of the medial wall to subdivide the Desikan unknown label? Just trying to think of some way to do this without dividing the unknown label by hand for each subject. Thanks in advance. Cheers, -Morgan

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calculation of total cortical gray matter volume
by Michael Harms 24 Jul '07

24 Jul '07

Hello FS-list, Could you please confirm the recommended current approach for calculating the total cortical gray matter volume. Based on the following Wiki page http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats? action=highlight&value=mris_volume I presume that the recommended calculation (illustrated using tcsh syntax) is: @ total_cort_gm_vol = `mris_volume ?h.pial` - `mris_volume ?h.white` My only hesitation is that I noticed the resulting value doesn't quite match the value of "total gray matter volume" that is output by mris_anatomical_stats. Is this because mris_anatomical_stats uses a older approach that is no longer considered quite as accurate? thanks, Mike Harms

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Problems downloading FSfast tutorial data
by McLean John (NHS Greater Glasgow & Clyde) 23 Jul '07

23 Jul '07

Hi, I am trying to download the FSfast tutorial data. So far i have been unsuccessful. I have tried downloading the files from IE and firefox browsers and also via ftp using filezilla, these have all failed. Am i doing something stupid or is it possible there is an issue at the source. Any help greatly appreciated. Best wishes John ********************************************************************** This message may contain confidential and privileged information. If you are not the intended recipient please accept our apologies. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Please inform us that this message has gone astray before deleting it. Thank you for your co-operation. NHSmail is used daily by over 100,000 staff in the NHS. Over a million messages are sent every day by the system. To find out why more and more NHS personnel are switching to this NHS Connecting for Health system please visit www.connectingforhealth.nhs.uk/nhsmail **********************************************************************

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Connecting Vertex Points in FreeSurfer
by Troy Mcan 20 Jul '07

20 Jul '07

Hi Everybody,I am bringing in talairach points into freesurfer by converting them into vertexes. I need to connect all of them to create a colored label showing the area bounded by these vertex points. However, I can't seem to find a way to connect these vertexes in a specified manner. I would greatly appreciate any help on the matter.Thanks!Best regards, _________________________________________________________________ PC Magazine’s 2007 editors’ choice for best web mail—award-winning Windows Live Hotmail. http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migrati…

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statistical designs
by Wang, Xin 20 Jul '07

20 Jul '07

Hello, group I want to learn more about designs of the general linear models for different statistical tests, such as paired T, ANOVA, and correlation tests. Could anybody suggest some examples of the designs for each model? I am facing a few problems of correlation analysis. If I want to do the within group correlation analysis, how can I do it without groups (or classes) as a regressor (if I only have one class and assign a 0 for the group in the contrast, does it work)? How can I specify the pearson's or Spearman's correlation in the analysis? How to know I have enough subjects for this correlation analysis? Thank you in advance, XIn Wang

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Skull Stripping Corrections
by James N. Porter 20 Jul '07

20 Jul '07

Hello- I've been working through the Skull Stripping checking/corrections tutorial and have a question. So far, I have found no problems akin to the tutorial, where skull is left behind or brain parts are missing. However, I do see remnants of eyeballs/eye sockets, arteries, and dura/pia/meninges. They don't seem too bad: http://www.tc.umn.edu/~norb0062/skull_strip_leftovers.bmp But I'm wondering how much trouble such remnants can cause down the pipeline. That is to say, when performing these checks should I only be concerned with making sure that all skull has been stripped away without taking away any brain, or should I also be concerned with making sure that all non-brain bits have been stripped away? -- Jim Porter TRiCAM Lab Coordinator Elliott Hall N437 612.624.3892 www.psych.umn.edu/research/tricam

2 1

Create thickness map
by Inês Souta 20 Jul '07

20 Jul '07

Hello, Is it possible to create a "fake" thickness map in order to perform some tests? Thanks, Ines

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How to analysis animal data
by lan lin 20 Jul '07

20 Jul '07

I know someone here have successfully apply freesurfer on monkey. Do you mind to describe how you can do that? Freesurfer is closely related to human atlas. If you need to apply it on animal, like monkey, do you need to contruct a monkey atlas? Anything besides atlas that need to take care? thanks

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Intersecting surfaces (thickness = 0mm)
by Inge K. Amlien 20 Jul '07

20 Jul '07

Hello list, when I process on v3.05 I notice areas where the pial and wm surfaces intersect, giving cortical thickness = 0. This is usually seen in the medial temporal area. Is this a known issue, and how should I deal with it? See attached screenshots. Have a nice day Inge Amlien Department of Psychology University of Oslo ------------------------------ Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.5 RedHat release: Red Hat Enterprise Linux WS release 4 (Nahant Update 5) Kernel info: Linux 2.6.9-42.0.10.ELsmp x86_64 (Hugging Linux)

2 1

mris_volmask
by Ipek Oguz 19 Jul '07

19 Jul '07

Hi, Where can I get the mris_volmask tool? I've seen that it was on the ftp server under pub/dist at some point, but it seems to have disappeared. Thanks a lot! -ipek

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Freesurfer July 2007